OpenMS  3.0.0
IDConflictResolver

Resolves ambiguous annotations of features with peptide identifications.

potential predecessor tools $ \longrightarrow $ IDConflictResolver $ \longrightarrow $ potential successor tools
IDMapper TextExporter
FeatureLinkerUnlabeled
(or another feature grouping algorithm)
ProteinQuantifier

The peptide identifications are filtered so that only one identification with a single hit (with the best score) is associated to each feature. (If two IDs have the same best score, either one of them may be selected.)

The the filtered identifications are added to the vector of unassigned peptides and also reduced to a single best hit.

This step may be useful before applying ProteinQuantifier, because features with ambiguous annotation are not considered for the quantification.

The command line parameters of this tool are:

IDConflictResolver -- Resolves ambiguous annotations of features with peptide identifications
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_IDConflictResolver.html
Version: 3.0.0-pre-nightly-2022-07-20 Jul 21 2022, 00:07:28, Revision: ea0316e
To cite OpenMS:
  Rost HL, Sachsenberg T, Aiche S, Bielow C et al.. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Meth. 2016; 13, 9: 741-748. doi:10.1038/nmeth.3959.

Usage:
  IDConflictResolver <options>

Options (mandatory options marked with '*'):
  -in <file>*                                           Input file (data annotated with identifications) (val
                                                        id formats: 'featureXML', 'consensusXML')
  -out <file>*                                          Output file (data with one peptide identification 
                                                        per feature) (valid formats: 'featureXML', 'consensus
                                                        XML')
  -resolve_between_features <resolve_between_features>  A map may contain multiple features with both identic
                                                        al (possibly modified i.e. not stripped) sequence
                                                        and charge state. The feature with the 'highest inten
                                                        sity' is very likely the most reliable one. When swit
                                                        ched on, the filter removes the sequence annotation
                                                        from the lower intensity features, thereby resolving
                                                        the multiplicity. Only the most reliable features
                                                        for each (possibly modified i.e. not stripped) sequen
                                                        ce maintain annotated with this peptide sequence.
                                                        (default: 'off' valid: 'off', 'highest_intensity')
                                                        
Common TOPP options:
  -ini <file>                                           Use the given TOPP INI file
  -threads <n>                                          Sets the number of threads allowed to be used by the 
                                                        TOPP tool (default: '1')
  -write_ini <file>                                     Writes the default configuration file
  --help                                                Shows options
  --helphelp                                            Shows all options (including advanced)

INI file documentation of this tool:

Legend:
required parameter
advanced parameter
+IDConflictResolverResolves ambiguous annotations of features with peptide identifications
version3.0.0-pre-nightly-2022-07-20 Version of the tool that generated this parameters file.
++1Instance '1' section for 'IDConflictResolver'
in Input file (data annotated with identifications)input file*.featureXML,*.consensusXML
out Output file (data with one peptide identification per feature)output file*.featureXML,*.consensusXML
resolve_between_featuresoff A map may contain multiple features with both identical (possibly modified i.e. not stripped) sequence and charge state. The feature with the 'highest intensity' is very likely the most reliable one. When switched on, the filter removes the sequence annotation from the lower intensity features, thereby resolving the multiplicity. Only the most reliable features for each (possibly modified i.e. not stripped) sequence maintain annotated with this peptide sequence.off,highest_intensity
log Name of log file (created only when specified)
debug0 Sets the debug level
threads1 Sets the number of threads allowed to be used by the TOPP tool
no_progressfalse Disables progress logging to command linetrue,false
forcefalse Overrides tool-specific checkstrue,false
testfalse Enables the test mode (needed for internal use only)true,false